Clostridium innocuum infection in hospitalised patients with inflammatory bowel disease

Fecal microbiota transplantation for vancomycin-resistant Clostridium innocuum infection in inflammatory bowel disease: A pilot study evaluating safety and clinical and microbiota outcome

BACKGROUND

Clostridium innocuum is a vancomycin-resistant pathobiome associated with poor clinical outcomes in inflammatory bowel disease (IBD). In ulcerative colitis (UC), it correlates with reduced remission rates, while in Crohn's disease (CD), it is linked to creeping fat formation and intestinal strictures. Notably, some patients experience refractory or recurrent C. innocuemailum infections despite metronidazole treatment. This study evaluates the safety and efficacy of single-dose fecal microbiota transplantation (FMT) in IBD patients with refractory or recurrent C. innocuum infections.

METHODS

We conducted a feasibility pilot study involving seven IBD patients (3 CD, 4 UC) with refractory (n = 5) or recurrent (n = 2) C. innocuum infections following metronidazole treatment. Patients underwent single-dose FMT and were monitored for six months.

RESULTS

No adverse events were recorded. All participants demonstrated improved disease activity post-FMT, as assessed by the Crohn's Disease Activity Index and Mayo Score. However, a mild increase in symptom severity was noted at six months. Follow-up cultures showed persistent C. innocuum infection in one patient and asymptomatic recurrence in another at three months. Alpha diversity of the gut microbiome increased post-FMT, and Bray-Curtis dissimilarity analysis revealed a microbiota composition more similar to that of the donor.

CONCLUSION

Single-dose FMT appears to be a safe and feasible therapeutic approach for refractory or recurrent C. innocuum infections in IBD patients, with potential benefits in disease activity and microbiome restoration. Further studies are warranted to optimize long-term outcomes.

FLZ attenuates Parkinson's disease pathological damage by increasing glycoursodeoxycholic acid production via down-regulating Clostridium innocuu m

Increasing evidence shows that the early lesions of Parkinson's disease (PD) originate from gut, and correction of microbiota dysbiosis is a promising therapy for PD. FLZ is a neuroprotective agent on PD, which has been validated capable of alleviating microbiota dysbiosis in PD mice. However, the detailed mechanisms still need elucidated. Through metabolomics and 16S rRNA analysis, we identified glycoursodeoxycholic acid (GUDCA) was the most affected differential microbial metabolite by FLZ treatment, which was specially and negatively regulated by Clostridium innocuum, a differential microbiota with the strongest correlation to GUDCA production, through inhibiting bile salt hydrolase (BSH) enzyme. The protection of GUDCA on colon and brain were also clarified in PD models, showing that it could activate Nrf2 pathway, further validating that FLZ protected dopaminergic neurons through promoting GUDCA production. Our study uncovered that FLZ improved PD through microbiota-gut-brain axis, and also gave insights into modulation of microbial metabolites may serve as an important strategy for treating PD.

Protective effect of low-dose lactulose in dextran sulfate sodium induced ulcerative colitis model of rats

Although low-dose lactulose has shown a good theoretical foundation for the treatment of ulcerative colitis (UC) in previous studies, the exact effects and mechanism remain unclear. The rats were randomly distributed into 5 groups, i.e., normal drinking water was provided for an initial 14 days in blank control group, 4% dextran sulfate sodium was used for modeling in the remaining 4 groups. During the 15-24th day, rats in the blank control group were administered with 0.9% saline (0.5 ml/d) by gavage. In the rest 4 groups, rats were administered 0.9% saline (0.5 ml/d, UC model), mesalazine (400 mg/kg/d), lactulose (1000 mg/kg/d), and lactulose + mesalazine (two-drug combination) by gavage. In addition to symptoms and pathological changes, serum IL-6, TNF-α, and High-sensitivity C-reactive protein(Hs-CRP) by ELISA analysis, mRNA and protein expression levels of TLR-2, TLR-4, Nuclear factor-κB(NF-κB), IL-6, and TNF-α in colon tissues by RT-qPCR and WB analyses respectively. Meanwhile, short-chain fatty acid(SCFAs) and intestinal flora were analyzed. Low-dose lactulose improved symptoms (diarrhea, blood in stool, weight loss) and pathological inflammation. In addition to serum IL-6, TNF-α, and Hs-CRP, the mRNA and protein expression levels of TLR-2, TLR-4, NF-κB, IL-6 and TNF-α in the colon were down-regulated with the intervention of lactulose.Meanwhile, lactulose decreased the ileocecal PH, increased SCFAs and altered the intestinal flora. Low-dose lactulose may be beneficial to UC by regulating TLRs/NF-κB pathway, reducing ileocecal PH, increasing SCFAs, regulating intestinal flora and improving the intestinal mucosal barrier. Meanwhile, low-dose lactulose and mesalazine may have additive effects upon combination.

Creeping fat and gut microbiota in Crohn's disease

In this article, we explored the role of adipose tissue, especially mesenteric adipose tissue and creeping fat, and its association with the gut microbiota in the pathophysiology and progression of Crohn's disease (CD). CD is a form of inflammatory bowel disease characterized by chronic inflammation of the gastrointestinal tract, influenced by genetic predisposition, gut microbiota dysbiosis, and environmental factors. Gut microbiota plays a crucial role in modulating immune response and intestinal inflammation and is associated with the onset and progression of CD. Further, visceral adipose tissue, particularly creeping fat, a mesenteric adipose tissue characterized by hypertrophy and fibrosis, has been implicated in CD pathogenesis, inflammation, and fibrosis. The bacteria from the gut microbiota may translocate into mesenteric adipose tissue, contributing to the formation of creeping fat and influencing CD progression. Although creeping fat may be a protective barrier against bacterial invasion, its expansion can damage adjacent tissues, leading to complications. Modulating gut microbiota through interventions such as fecal microbiota transplantation, probiotics, and prebiotics has shown potential in managing CD. However, more research is needed to clarify the mechanisms linking gut dysbiosis, creeping fat, and CD progression and develop targeted therapies for microbiota modulation and fat-related complications in patients with CD.

Itaconic Acid Alleviates Perfluorooctanoic Acid-Induced Oxidative Stress and Intestinal Damage by Regulating the Keap1/Nrf2/Ho-1 Pathway and Reshaping the Gut Microbiota

Itaconic acid (IA) is recognized for its potential application in treating intestinal diseases owing to the anti-inflammatory and antioxidant properties. Perfluorooctanoic acid (PFOA) can accumulate in animals and result in oxidative and inflammatory damages to multi-tissue and organ, particularly in the intestinal tract. This study aimed to explore whether IA could mitigate intestinal damage induced by PFOA exposure in laying hens and elucidate its potential underlying mechanisms. The results showed that IA improved the antioxidant capacity of laying hens and alleviated the oxidative damage induced by PFOA, as evidenced by the elevated activities of T-SOD, GSH-Px, and CAT, and the decreased MDA content in both the jejunum and serum. Furthermore, IA improved the intestinal morphological and structural integrity, notably attenuating PFOA-induced villus shedding, length reduction, and microvillus thinning. IA also upregulated the mRNA expression of ZO-1, Occludin, Claudin-1, and Mucin-2 in the jejunum, thereby restoring intestinal barrier function. Compared with the PF group, IA supplementation downregulated the gene expression of Keap1 and upregulated the HO-1, NQO1, SOD1, and GPX1 expression in the jejunum. Meanwhile, the PF + IA group exhibited lower expressions of inflammation-related genes (NF-κB, IL-1β, IFN-γ, TNF-α, and IL-6) compared to the PF group. Moreover, IA reversed the PFOA-induced imbalance in gut microbiota by reducing the harmful bacteria such as Escherichia-Shigella, Clostridium innocuum, and Ruminococcus torques, while increasing the abundance of beneficial bacteria like Lactobacillus. Correlation analysis further revealed a significant association between gut microbes, inflammatory factors, and the Keap1/Nrf2/HO-1 pathway expression. In conclusion, dietary IA supplementation could alleviate the oxidative and inflammatory damage caused by PFOA exposure in the intestinal tract by reshaping the intestinal microbiota, modulating the Keap1/Nrf2/HO-1 pathway and reducing oxidative stress and inflammatory response, thereby promoting intestinal homeostasis.

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial

Even though dietary fibres are often used as prebiotic supplements in dogs, the effect of individual types of fibres on canine microbiota composition is unknown. The objective of this study was to assess changes in faecal microbiota richness, diversity and taxonomic abundance with three different fibre supplements in dogs. These were psyllium husk, resistant starch from banana flour and methylcellulose. They were administered to 17 healthy dogs in a cross-over trial after transition to the same complete feed. Faecal scores and clinical activity indices were recorded, and faecal samples were collected before and at the end of supplementation, as well as 2 weeks after each supplement (washout). Illumina NovaSeq paired-end 16S rRNA gene sequencing was performed on all samples. After quality control and chimera removal, alpha diversity indices were calculated with QIIME. Differences in specific taxa between groups were identified using Metastats. Methylcellulose significantly increased faecal scores but had no effect on microbiota. Psyllium resulted in minor changes in the abundance of specific taxa, but with questionable biological significance. Resistant starch reduced microbiota richness and resulted in the most abundant changes in taxa, mostly a reduction in short-chain fatty acid-producing genera of the phylum Bacillota, with an increase in genera within the Bacteroidota, Pseudomonadota, Actinomycetota and Saccharibacteria. In conclusion, while psyllium and methylcellulose led to few changes in the microbiota composition, the taxonomic changes seen with resistant starch may indicate a less favourable composition. Based on this, the type of resistant starch used here cannot be recommended as a prebiotic in dogs.

Clostridium innocuum, an emerging pathogen that induces lipid raft-mediated cytotoxicity

Clostridium innocuum is an emerging spore-forming anaerobe that is often observed in Clostridioides difficile-associated inflammatory bowel disease (IBD) exacerbations. Unlike C. difficile, C. innocuum neither produces toxins nor possesses toxin-encoding genetic loci, but is commonly found in both intestinal and extra-intestinal infections. Membrane lipid rafts are composed of dynamic assemblies of cholesterol and sphingolipids, allowing bacteria to gain access to cells. However, the direct interaction between C. innocuum and lipid rafts that confers bacteria the ability to disrupt the intestinal barrier and induce pathogenesis remains unclear. In this study, we investigated the associations among nucleotide-binding oligomerization domain containing 2 (NOD2), lipid rafts, and cytotoxicity in C. innocuum-infected gut epithelial cells. Our results revealed that lipid rafts were involved in C. innocuum-induced NOD2 expression and nuclear factor (NF)-κB activation, triggering an inflammatory response. Reducing cholesterol by simvastatin significantly dampened C. innocuum-induced cell death, indicating that the C. innocuum-induced pathogenicity of cells was lipid raft-dependent. These results demonstrate that NOD2 mobilization into membrane rafts in response to C. innocuum-induced cytotoxicity results in aggravated pathogenicity.

Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts

The perturbations of the gut microbiota and metabolites are closely associated with the progression of inflammatory bowel disease (IBD). However, inconsistent findings across studies impede a comprehensive understanding of their roles in IBD and their potential as reliable diagnostic biomarkers. To address this challenge, here we comprehensively analyze 9 metagenomic and 4 metabolomics cohorts of IBD from different populations. Through cross-cohort integrative analysis (CCIA), we identify a consistent characteristic of commensal gut microbiota. Especially, three bacteria, namely Asaccharobacter celatus, Gemmiger formicilis, and Erysipelatoclostridium ramosum, which are rarely reported in IBD. Metagenomic functional analysis reveals that essential gene of Two-component system pathway, linked to fecal calprotectin, are implicated in IBD. Metabolomics analysis shows 36 identified metabolites with significant differences, while the roles of these metabolites in IBD are still unknown. To further elucidate the relationship between gut microbiota and metabolites, we construct multi-omics biological correlation (MOBC) maps, which highlights gut microbial biotransformation deficiencies and significant alterations in aminoacyl-tRNA synthetases. Finally, we identify multi-omics biomarkers for IBD diagnosis, validated across multiple global cohorts (AUROC values ranging from 0.92 to 0.98). Our results offer valuable insights and a significant resource for developing mechanistic hypotheses on host-microbiome interactions in IBD.

Bacteremia due to Clostridium innocuum: Analysis of four cases and literature review

Clostridium innocuum is a Gram-positive anaerobic spore-forming bacillus that has been identified as part of the normal intestinal microbiota. This bacterium has been rarely associated with human infections, and only few severe infections have been reported until now. In this work, we report on four patients with bacteremia due to C. innocuum, which were well identified by MALDI-TOF MS. Moreover, a review of the previous published cases of bacteremia due to this anaerobic bacterium has been performed.

Inflammatory bowel disease complicated with rare pathogen infection

As an autoimmune disease, inflammatory bowel disease (IBD) is characterized by a chronic disease course and recurrent episodes. The prognosis of patients with IBD complicated with infection is poor. At present, there are many reports on IBD complicated with infection by common pathogen such as Clostridium difficile, Mycobacterium tuberculosis, Escherichia coli and hepatitis viruses both in China and other contries, but there are few reviews on IBD complicated with infection by rare pathogens. Based on this, this article reviews rare pathogen infection in IBD.

Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection

Background

Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.

Methods

We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.

Results

We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.

Conclusion

IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.

Do we need to change our perspective about gut biomarkers? A public data mining approach to identify differentially abundant bacteria in intestinal inflammatory diseases

Introduction

The gut microbiome is involved in multiple processes that influence host physiology, and therefore, disruptions in microbiome homeostasis have been linked to diseases or secondary infections. Given the importance of the microbiome and the communities of microorganisms that compose it (microbiota), the term biomarkers were coined, which are bacteria correlated with disease states, diets, and the lifestyle of the host. However, a large field in the study of intestinal biomarkers remains unexplored because the bacterial communities associated with a given disease state have not been exactly defined yet.

Methods

Here, we analyzed public data of studies focused on describing the intestinal microbiota of patients with some intestinal inflammatory diseases together with their respective controls. With these analyses, we aimed to identify differentially abundant bacteria between the subjects with the disease and their controls.

Results

We found that frequently reported bacteria such as Fusobacterium, Streptococcus, and Escherichia/Shigella were differentially abundant between the groups, with a higher abundance mostly in patients with the disease in contrast with their controls. On the other hand, we also identified potentially beneficial bacteria such as Faecalibacterium and Phascolarctobacterium, with a higher abundance in control patients.

Discussion

Our results of the differentially abundant bacteria contrast with what was already reported in previous studies on certain inflammatory diseases, but we highlight the importance of considering more comprehensive approaches to redefine or expand the definition of biomarkers. For instance, the intra-taxa diversity within a bacterial community must be considered, as well as environmental and genetic factors of the host, and even consider a functional validation of these biomarkers through in vivo and in vitro approaches. With the above, these key bacterial communities in the intestinal microbiota may have potential as next-generation probiotics or may be functional for the design of specific therapies in certain intestinal diseases.

Radiation Exposure among Patients with Inflammatory Bowel Disease: A Single-Medical-Center Retrospective Analysis in Taiwan

Inflammatory bowel disease (IBD) is a chronic and relapsing disease that can be complicated by abscesses, fistulas, or strictures of the damaged bowel. Endoscopy or imaging studies are required to diagnose and monitor the treatment response or complications of the disease. Due to the low incidence of the disease in Taiwan, the pattern of radiation exposure from medical imaging has not been well studied previously. This retrospective study aimed to evaluate the pattern of radiation exposure in 134 Taiwanese IBD patients (45 CD and 89 UC) diagnosed and followed at Changhua Christian Hospital from January 2010 to December 2020. We reviewed the patient demographic data and radiation-containing image studies performed during the follow-up. The cumulative effective dose (CED) was calculated for each patient. During a median follow-up of 4 years, the median CED was higher for patients with CD (median CED 21.2, IQR 12.1−32.8) compared to patients with UC (median CED 2.1, IQR 0−5.6) (p < 0.001). In addition, the CD patients had a trend of a higher rate of cumulative ≥50 mSv compared with the UC patients (6.7% vs. 1.1%, p = 0.110). In conclusion, our study found a higher radiation exposure among CD patients compared to patients with UC, representing the complicated nature of the disease. Therefore, increasing the use of radiation-free medical imaging such as intestinal ultrasound or magnetic resonance imaging should be advocated in daily practice to decrease the risk of excessive radiation exposure in these patients.